DOCK 3.8:How to build a release

This page describes the formal definition of a release of the UCSF DOCK software suite

Build pydock3 Python package

• (e.g., build pip-installable wheel file using poetry).
• this can all be done on gimel2
• git clone https://github.com/docking-org/pydock3.git
• cd pydock3
• git submodule update --init --recursive. #why? dock3 is a submodule of pydock3. We need to tell git this.

( you need to authenticate, and you need to have generated token)

• use the generated token as your password
• run poetry, e.g.
• ~isknight/.local/bin/poetry build
• if there is a general python venv ready, use it. Else create new python venv (see below)
• e.g. source myvenv/bin/activate
• pip install dist/pydock3-0.1.0rc1-py3-none-any.whl

(optional) create new python venv

• https://wiki.docking.org/index.php/Create_venv

Make a fresh and clean dock3 executable

• git clone https://github.com/docking-org/dock3.git
• ssh psi
• bash
• export PATH=/nfs/soft/pgi/current/linux86-64/12.10/bin:$PATH
• source /nfs/home/tbalius/zzz.virtualenvs/virtualenv-1.9.1/myVEonGimel/bin/activate
• source /nfs/soft/pgi/env.sh
• verify that compiler set to pgf95 in Makefiles
• cd into libfgz
• make clean; make
• cd into i386
• make clean; make

Get the 3D building pipeline

• git clone https://github.com/docking-org/zinc22-3d.git
• instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22
• git clone https://github.com/docking-org/zinc22-3d-submit.git
• mv zinc22-3d-submit zinc22-3d/bin
• yeah, ok, this is funky, we will clean it up
• git clone https://github.com/docking-org/SUBDOCK.git
• mv SUBDOCK DOCK3.8/bin

Incorporate the fruits of (1), (2) and (3) into DOCK3.8 repository housing an arsenal of scripts

• (e.g., 3D build scripts, post-processing scripts) that are essential for following the published Nature protocol.
• mkdir DOCK3.8 # create an empty shell
• cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts
• cp dock3/src/i386/dock64 DOCK3.8 # copy in optimized executable
• tar czf DOCK3.8/zinc22-3d.tgz zinc22-3d
• the release is now ready. create a tarball.
• tar czf dock_3.8.x.tar.gz DOCK3.8

Distribution

• put on DOCK license server
• copy dock3.8.x.tar.gz to dock server. test download and install
• put on gimel
• same
• put on wynton
• same
• put in dockingorg/awsdock
• bin and dock64

Testing at point of installation

• test on DOCK license server (download, install, follow instructions)
• installation instructions....
• test on gimel2
• test on wynton
• test on AWS

once tested, clean up old versions so the correct version to use is unambiguous.

A particular commit of the DOCK3.8 repository formally becomes a particular distribution of UCSF DOCK software when the commit is tagged with the distribution's semantic version (e.g., DOCK3.8 v1.2.0). Note that pydock3 and dock3 are separately versioned from DOCK3.8.